org.openscience.cdk.qsar.descriptors.atomic
Class AtomHybridizationVSEPRDescriptor

java.lang.Object
  org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptorTest")
public class AtomHybridizationVSEPRDescriptor
extends Object
implements IAtomicDescriptor

This class returns the hybridization of an atom.

This class try to find a SIMPLE WAY the molecular geometry for following from Valence Shell Electron Pair Repulsion or VSEPR model and at the same time its hybridization of atoms in a molecule.

The basic premise of the model is that the electrons are paired in a molecule and that the molecule geometry is determined only by the repulsion between the pairs. The geometry adopted by a molecule is then the one in which the repulsions are minimized.

It counts the number of electron pairs in the Lewis dot diagram which are attached to an atom. Then uses the following table.

 

   
  
          
pairs on an atom
    
hybridization of the atom
    
geometry
    
number for CDK.Constants
 
   
   
   
2
sp
linear
1
   
3
sp^2
trigonal planar
2
   
4
sp^3
tetrahedral
3
   
5
sp^3d
trigonal bipyramid
4
   
6
sp^3d^2
octahedral
5
   
7
sp^3d^3
pentagonal bipyramid
6
   
8
sp^3d^4
square antiprim
7
   
9
sp^3d^5
tricapped trigonal prism
8
 
 

This table only works if the central atom is a p-block element (groups IIA through VIIIA), not a transition metal.

This descriptor uses these parameters:

Name	Default	Description
		no parameters

Author:

Miguel Rojas

Belongs to the set:

qsar-descriptors

Created on:

2005-03-24

Belongs to CDK module:

qsaratomic

Dictionary pointer(s):

atomHybridizationVSEPR in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:atomHybridizationVSEPR]

Source code:

cdk-1.4.x

Constructor Summary

AtomHybridizationVSEPRDescriptor()
Constructor for the AtomHybridizationVSEPRDescriptor object

Method Summary

DescriptorValue	calculate(IAtom atom, IAtomContainer container) This method calculates the hybridization of an atom.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object
Object[]	getParameters() Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object
void	setParameters(Object[] params) This descriptor does have any parameter.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AtomHybridizationVSEPRDescriptor

public AtomHybridizationVSEPRDescriptor()

Constructor for the AtomHybridizationVSEPRDescriptor object

Method Detail

getSpecification

@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification()

Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params)
                   throws CDKException

This descriptor does have any parameter.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - An array of Object containing the parameters for this descriptor

Throws:

CDKException - if invalid number of type of parameters are passed to it

See Also:

IDescriptor.getParameters()

getParameters

@TestMethod(value="testGetParameters")
public Object[] getParameters()

Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

getDescriptorNames

@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames()

Description copied from interface: IDescriptor

Returns an array of names for each descriptor value calculated.

Many descriptors return multiple values. In general it is useful for the descriptor to indicate the names for each value.

In many cases, these names can be as simple as X1, X2, ..., XN where X is a prefix and 1, 2, ..., N are the indices. On the other hand it is also possible to return other arbitrary names, which should be documented in the Javadocs for the decsriptor (e.g., the CPSA descriptor).

Note that by default if a descriptor returns a single value (such as ALOGPDescriptor the return array will have a single element

Specified by:

getDescriptorNames in interface IDescriptor

Returns:

An array of descriptor names, equal in length to the number of descriptor calculated..

calculate

@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom,
                                                 IAtomContainer container)

This method calculates the hybridization of an atom.

Specified by:

calculate in interface IAtomicDescriptor

Parameters:

atom - The IAtom for which the DescriptorValue is requested

container - Parameter is the atom container.

Returns:

The hybridization

getParameterNames

@TestMethod(value="testGetParameterNames")
public String[] getParameterNames()

Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name)

Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

An Object of class equal to that of the parameter being requested